Abstract
Milk and dairy products are rich in nutrients and are therefore habitats for various microbiomes. However, the composition of nutrients can be quite diverse, in particular among the sulfur containing amino acids. In milk, methionine is present in a 25-fold higher abundance than cysteine. Interestingly, a fraction of strains of the species L. paracasei – a flavor-enhancing adjunct culture species – can grow in medium with methionine as the sole sulfur source. In this study, we focus on genomic and evolutionary aspects of sulfur dependence in L. paracasei strains. From 24 selected L. paracasei strains, 16 strains can grow in medium with methionine as sole sulfur source. We sequenced these strains to perform gene-trait matching. We found that one gene cluster – consisting of a cysteine synthase, a cystathionine lyase, and a serine acetyltransferase – is present in all strains that grow in medium with methionine as sole sulfur source. In contrast, strains that depend on other sulfur sources do not have this gene cluster. We expanded the study and searched for this gene cluster in other species and detected it in the genomes of many bacteria species used in the food production. The comparison to these species showed that two different versions of the gene cluster exist in L. paracasei which were likely gained in two distinct events of horizontal gene transfer. Additionally, the comparison of 62 L. paracasei genomes and the two versions of the gene cluster revealed that this gene cluster is mobile within the species.
Highlights
Lactobacillus paracasei belongs to the lactic acid bacteria (LAB), which are gram-positive bacteria with lactic acid as the main product of the carbohydrate metabolism
To be a successful bacteria species in a medium such as milk, which is rich in the amount of nutrients, but rather limited in its diversity, it is indispensable for the bacterium to metabolize these substrates into essential compounds
We found that the cysK-ctl-cysE gene cluster is the most important gene cluster that allows L. paracasei strains to grow with methionine as sole sulfur source
Summary
Lactobacillus paracasei belongs to the LAB, which are gram-positive bacteria with lactic acid as the main product of the carbohydrate metabolism. It was suggested that the species L. paracasei has a large gene pool that allows the bacteria to adapt to the different habitats (Broadbent et al, 2012; Smokvina et al, 2013). Contrary to the natural habitats, the emergence of the milk and cheese as habitats is a rather recent event (Salque et al, 2013) These habitats are rich in nutrients like carbohydrates, proteins and lipids compared to natural habitats. It was proposed in earlier studies that the adaptation to the milk related habitats caused gene loss in L. paracasei (Cai et al, 2009)
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